Intellicount: High-throughput quantification of fluorescent synaptic protein puncta by machine learning

J. A. Fantuzzo, V. R. Mirabella, A. H. Hamod, R. P. Hart, J. D. Zahn, Zhiping P. Pang

Research output: Contribution to journalArticlepeer-review

27 Scopus citations


Synapse formation analyses can be performed by imaging and quantifying fluorescent signals of synaptic markers. Traditionally, these analyses are done using simple or multiple thresholding and segmentation approaches or by labor-intensive manual analysis by a human observer. Here, we describe Intellicount, a highthroughput, fully-automated synapse quantification program which applies a novel machine learning (ML)-based image processing algorithm to systematically improve region of interest (ROI) identification over simple thresholding techniques. Through processing large datasets from both human and mouse neurons, we demonstrate that this approach allows image processing to proceed independently of carefully set thresholds, thus reducing the need for human intervention. As a result, this method can efficiently and accurately process large image datasets with minimal interaction by the experimenter, making it less prone to bias and less liable to human error. Furthermore, Intellicount is integrated into an intuitive graphical user interface (GUI) that provides a set of valuable features, including automated and multifunctional figure generation, routine statistical analyses, and the ability to run full datasets through nested folders, greatly expediting the data analysis process.

Original languageEnglish (US)
Article numbere0219-17.2017
Issue number6
StatePublished - Nov 1 2017

All Science Journal Classification (ASJC) codes

  • Neuroscience(all)


  • Automated image analysis
  • High-throughput
  • Immunofluorescence
  • Machine learning
  • Synapse formation
  • Synapse quantification


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